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Biomedical subjects

G Stubbs

Publications and source records attributed to G Stubbs.

At least 19 recordsLinked to original sources
PubMed2000

Evaporative microdialysis: an effective improvement in an established method of protein crystallization.

Evaporative dialysis is a simple variant of conventional microdialysis in which the reservoir solution is allowed to evaporate slowly. The slow increase in precipitant concentration allows crystals to grow without increasing nucleation. The method is useful for proteins that have a very narrow metastable zone (the range of solution conditions under which crystals grow but nuclei do not form at an appreciable rate). The method is demonstrated with the coat protein of potato virus X.

Capsid↗
PubMed1999

Tobacco mosaic virus particle structure and the initiation of disassembly.

The structure of an intact tobacco mosaic virus (TMV) particle was determined at 2.9 A resolution using fibre diffraction methods. All residues of the coat protein and the three nucleotides of RNA that are bound to each protein subunit were visible in the electron density map. Examination of the structures of TMV, cucumber green mottle mosaic virus and ribgrass mosaic virus, and site-directed mutagenesis experiments in which carboxylate groups were changed to the corresponding amides, showed that initial stages of disassembly are driven by complex electrostatic interactions involving at least seven carboxylate side-chains and a phosphate group. The locations of these interactions can drift during evolution, allowing the viruses to evade plant defensive responses that depend on recognition of the viral coat protein surface.

Computer Simulation↗
PubMed1999

Developments in fiber diffraction.

Improved specimen preparation methods, third generation synchrotron sources, new data processing algorithms and molecular dynamics refinement techniques are, together, allowing the high-resolution structure determination of larger and larger macromolecular complexes by fiber diffraction. New synchrotron sources are also making possible both time-resolved studies and studies of ordered fibers only a few microns in diameter.

Animals↗
PubMed1998

Coat protein interactions involved in tobacco mosaic tobamovirus cross-protection.

To investigate the molecular role of the tobacco mosaic tobamovirus (TMV) coat protein (CP) in conferring cross-protection, a potato X potexvirus (PVX) vector (S. Chapman, Plant J. 2, 549-557, 1992) was used to systemically express a set of TMV mutant CPs in Nicotiana benthamiana prior to challenge inoculation with TMV. PVX-expressed wild-type TMV CP delayed TMV accumulation for up to 2 weeks compared to unprotected plants or plants preinfected with the unmodified PVX vector. Similar delays in TMV accumulation were obtained using TMV CPs that were deficient in virion formation but competent to assemble into helical aggregates. In contrast, TMV CPs that were incapable of helical aggregation or unable to bind viral RNA did not delay the accumulation of TMV. Furthermore, TMV CPs with enhanced intersubunit interactions that favor helical aggregation produced significantly greater delays in the accumulation of challenge TMV than obtained from the wild-type CP. Thus the capabilities of TMV CP to interact with viral RNA and self-associate in a helical fashion appear to be essential to its ability to confer protection. Taken together, these findings support a model for CP-mediated resistance in which the protecting CP recoats the challenge virus RNA as it disassembles.

Capsid Proteins↗
PubMed1998

Intersubunit interactions allowing a carboxylate mutant coat protein to inhibit tobamovirus disassembly.

Tobacco mosaic tobamovirus (TMV) coat protein (CP) mutant E50Q lacks a repulsive intersubunit carboxylate group and can effectively inhibit the disassembly of wild-type TMV (Culver et al, 1995, Virology 206,724). To investigate the ability of this mutant CP to block disassembly, a series of second-site amino acid substitutions were added to the E50Q CP. These second-site mutations were designed to disrupt specific intersubunit stabilizing interactions involving hydrophobic or polar residues, salt bridges, and CP-RNA contacts. Results showed substitutions disrupting intersubunit interactions that face the disassembling surface of the virion dramatically reduced the ability of CP E50Q to inhibit TMV disassembly. Substitutions that disrupted the CP inner loop, RNA binding capabilities, or intersubunit interactions that faced away from the disassembling surface did not dramatically interfere with CP E50Q's ability to inhibit disassembly. Taken together, these findings suggest that intersubunit interactions made by 5' terminal E50Q subunits, not associated with RNA, provide the stabilizing forces that prevent virion disassembly. The role of these stabilizing interactions in TMV disassembly and their potential use for creating disassembly inhibiting CPs are discussed.

Capsid↗
PubMed1998

Caspar carboxylates: the structural basis of tobamovirus disassembly.

Carboxylate groups have been known for many years to drive the disassembly of simple viruses, including tobacco mosaic virus (TMV). The identities of the carboxylate groups involved and the mechanism by which they initiate disassembly have not, however, been clear. Structures have been determined at resolutions between 2.9 and 3.5 A for five tobamoviruses by fiber diffraction methods. Site-directed mutagenesis has also been used to change numerous carboxylate side chains in TMV to the corresponding amides. Comparison of the stabilities of the various mutant viruses shows that disassembly is driven by a much more complex set of carboxylate interactions than had previously been postulated. Despite the importance of the carboxylate interactions, they are not conserved during viral evolution. Instead, it appears that during evolution, patches of electrostatic interaction drift across viral subunit interfaces. The flexibility of these interactions confers a considerable advantage on the virus, enabling it to change its surface structure rapidly and thus evade host defenses.

Binding Sites↗
PubMed1997

Structure of ribgrass mosaic virus at 2.9 A resolution: evolution and taxonomy of tobamoviruses.

Ribgrass mosaic virus (RMV) is a member of the tobamovirus group of plant viruses. The structure has been determined at 2.9 A resolution by fiber diffraction methods, and refined by molecular dynamics methods to an R-factor of 0.095. The carboxyl-carboxylate interactions that drive disassembly in tobamoviruses are present in RMV, but are very different from those in other tobamoviruses. RMV has some of the structural features of a subgroup I tobamovirus, a smaller number from subgroup II, and a number that appear to be unique to the RMV cluster of viruses. The structural studies confirm the evolutionary and taxonomic separation of the RMV cluster from both subgroup I and subgroup II tobamoviruses.

Amino Acid Sequence↗
PubMed1996

Carboxylate interactions involved in the disassembly of tobacco mosaic tobamovirus.

Structural studies of tobacco mosaic tobamovirus (TMV) have identified two coat protein (CP) intersubunit carboxyl-carboxylate interactions and one CP carboxylate-RNA phosphate interaction whose electrostatic repulsion is believed to drive virion disassembly. In this study, the involvement of each interaction in the disassembly process was examined. Site-directed mutagenesis was used to replace selected negatively charged CP residues, E or D, with neutral residues, Q or N, respectively. Purified mutant CPs were assayed for their ability to inhibit wild-type TMV disassembly both in vitro and in vivo. Results indicate that the lateral carboxylate interaction made by residue E106 is much more complex than previously thought, involving three residues, E95, E97, and D109, from an adjacent subunit. Mutations at all three residues are required to inhibit disassembly significantly. Different mutant coat proteins inhibited disassembly of the wild-type virus to varying degrees. Mutant E50Q, which modified the axial intersubunit interaction, had the greatest ability to inhibit disassembly followed by mutants E95Q/E97Q/D109N and D116N, which modified the lateral and CP-RNA interactions, respectively. Within each set of interacting carboxylate groups, mutations in the face opposite the disassembling surface of the TMV virion conferred the greatest ability to inhibit disassembly. This observation is consistent with the polar nature of TMV disassembly and confirms that repulsive intersubunit interactions derived from the 5' terminal subunits provide the key controlling mechanisms for virion disassembly.

Capsid↗
PubMed1995

Site-directed mutagenesis confirms the involvement of carboxylate groups in the disassembly of tobacco mosaic virus.

Electrostatic repulsion between carboxylate groups across subunit interfaces has for many years been recognized as important in the disassembly of simple plant viruses. In the coat protein of tobacco mosaic virus (TMV), the amino acids Glu50 and Asp77 have been proposed as examples of such carboxylate groups. Site-directed mutagenesis has been used to replace these amino acids by Gln and Asn, respectively. Increased virion stability, together with reduced infectivity and reduced capacity for long-distance transport within the host plant confirms that the negative charges on the side chains of these amino acids are involved in the disassembly of TMV. Mixing purified mutant coat proteins with wild-type virions under appropriate conditions stabilizes the virions to alkaline disassembly and reduces their infectivity. It is suggested that transgenic plants expressing such mutant coat proteins could have enhanced resistance to virus infection.

Capsid↗
PubMed1994

Structure-function relationship between tobacco mosaic virus coat protein and hypersensitivity in Nicotiana sylvestris.

Alterations in the structure of the tobacco mosaic virus (TMV) coat protein affect the elicitation of the N' gene hypersensitive response (HR) in Nicotiana sylvestris. To investigate this structure-function relationship, amino acid substitutions with predicted structural effects were created throughout the known structure of the TMV coat protein. Substitutions that resulted in the elicitation of the HR resided within and would predictably interfere with interface regions located between adjacent subunits in ordered aggregates of coat protein. Substitutions that did not result in the elicitation of the HR were either conservative or located outside these interface regions. In vitro analysis of coat protein aggregates demonstrated HR-eliciting coat proteins to have reduced aggregate stability in comparison with non-HR-eliciting coat proteins and a correlation existed between the strength of the elicited HR and the ability of a substitution to interfere with ordered aggregate formation. This finding corresponded with the predicted structural effects of HR-eliciting substitutions. Radical substitutions that predictably disrupted coat protein tertiary structure were found to prevent HR elicitation. These findings demonstrate that structural alterations that affect the stability of coat protein quaternary structure but not tertiary structure lead to host cell recognition and HR elicitation. A model for HR elicitation is proposed, in which disassembly of coat protein aggregates exposes a host "receptor" binding site.

Amino Acids↗
PubMed1994

Structure determination of cucumber green mottle mosaic virus by X-ray fiber diffraction. Significance for the evolution of tobamoviruses.

Cucumber green mottle mosaic virus (CGMMV) is a rod-shaped virus of the tobacco mosaic virus (TMV) group. The structure of cucumber green mottle mosaic virus has been determined by fiber diffraction methods at 3.4 A resolution, and refined by molecular dynamics methods to an R factor of 0.093. Disassembly of TMV is driven by the mutual repulsion of intersubunit carboxyl-carboxylate pairs, but one of these pairs is not conserved in CGMMV. An alternative pair, located about 5 A from the site of the TMV pair, has been found in CGMMV. Comparison of the two structures suggests that the carboxylate groups are free to migrate in the subunit interfaces during evolution.

Biological Evolution↗
PubMed1993

Crystallization and preliminary X-ray analysis of papaya mosaic virus coat protein.

Papaya mosaic virus coat protein has been treated with trypsin and a large fragment of the intact protein has been crystallized in space group P3(1)21 or P3(2)21 (unit cell dimensions: a = b = 110 A, c = 237 A). The crystals diffract to 3.5 A resolution. Crystals of the untreated protein have also been grown. The untreated protein crystals diffract to 4 A resolution, but have a large mosaic spread. They have the same space group as the trypsin-treated protein crystals, but a much smaller unit cell (a = b = 72 A, c = 240 A).

Capsid↗
PubMed1993

Preliminary X-ray diffraction studies of ribgrass mosaic virus.

Fiber diffraction data were collected from oriented sols of ribgrass mosaic virus and a lead derivative of the virus. Two lead binding sites were found. Two intersubunit carboxylcarboxylate pairs, different from those in other tobamoviruses, are predicted to control viral assembly and disassembly. One of the carboxyl-carboxylate pairs forms part of a lead binding site.

Amino Acid Sequence↗
PubMed1993

Molecular dynamics in refinement against fiber diffraction data.

The molecular dynamics (MD) method has been adapted for refinement of the structures of helical macromolecular aggregates aginst X-ray fiber diffraction data. To test the effectiveness of the method, refinements of the tobacco mosaic virus structure were carried out against a set of simulated fiber diffraction intensities using the MD method as well as the conventional restrained least-squares (RLS) method. The MD refinement converged to a very low R factor and produced a structure with generally satisfactory sterochemistry, while the RLS refinemnt was trapped at a local energy minimum with a larger R factor. Results suggest that the effective experimental radius of convergence of the MD method is significantly greater than that of the RLS method. Even when the initial structure is too far from the true structure to allow direct refinement, the MD method is able to find local minima that resemble the true structure sufficiently to allow improved phasing and thus lead to interpretable difference maps for model rebuilding.

Capsid↗
PubMed1992

Structure of the U2 strain of tobacco mosaic virus refined at 3.5 A resolution using X-ray fiber diffraction.

The structure of the U2 strain of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 3.5 A resolution, and refined by a combination of restrained least-squares and molecular dynamics methods to an R-factor of 0.096. The structure is extremely similar to that of the common strain of TMV, with the largest differences being in the protein loop that makes up the inner surface of the virus, and in the C-terminal region on the outer surface. Differences in the inner loop can be correlated with differences in the properties of the two viruses.

Capsid↗
PubMed1992

Characterization of a putative calcium-binding site in tobacco mosaic virus.

Lead has been used as a substitute for calcium binding to tobacco mosaic virus (TMV). The high atomic number of lead has allowed us to use difference maps from X-ray fiber diffraction data to characterize a calcium-binding site in the virus. The metal ligands are slightly different from those previously believed to bind calcium to TMV, although the binding site is very close to one previously described. Two acetate groups are also bound to the lead atom. There is no significant backbone conformational change in the protein as a result of metal binding; the binding is accomplished by means of relatively small movements in amino acid side chains.

Binding Sites↗
PubMed1990

Fiber diffraction analysis of cucumber green mottle mosaic virus using limited numbers of heavy-atom derivatives.

The structure of cucumber green mottle mosaic virus has been determined from fiber diffraction data to a resolution of 5 A, using only two derivatives and without making any specific assumptions about the molecular structure of the virus. Because of the cylindrical averaging of fiber diffraction data, large numbers of heavy-atom derivatives have been required in previous structure determinations, but it is shown that simplifying assumptions about the overlapping intensities in fiber diffraction are sufficient for structure determination at this resolution using only two derivatives.

Image Processing, Computer-Assisted↗